User: User 9334

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User 933460
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Last seen:
8 years, 1 month ago
Joined:
8 years, 1 month ago
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u3898

Posts by User 9334

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Comment: C: Getting Pairwise Genome Alignments/Syntenic Regions From Ensembl Or Ucsc?
... The net format from UCSC is horrendous are there simpler pairwise alignments that can be used between human mouse? Ensembl must have this information somewhere but I cannot find a way to download it. ANy ideas? ...
written 8.1 years ago by User 933460
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Getting Pairwise Genome Alignments/Syntenic Regions From Ensembl Or Ucsc?
... This should be trivial but i cannot find the answer on the ensembl website, which just sends the user in circles. i'm trying to download pairwise genome alignments and/or list of syntenic regions (eg between human and mouse) -- without going through any API. the ensembl website refers to various pai ...
ensembl comparative ucsc written 8.1 years ago by User 933460 • updated 8.1 years ago by Bert Overduin3.7k
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Comment: C: Finding Homologous Exons Between Species Using Pycogent
... the interface to ensembl makes this information extremely difficult to find. where can i download the ensembl compara from, without downloading all of ensembl? if i want to get all the mouse / human alignments or syntenic regions for example, where can this be downloaded through biomart? thank you ...
written 8.1 years ago by User 933460
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Finding Homologous Exons Between Species Using Pycogent
... i have a set of exon coordinates in human that i want to find the orthologs of in mouse, and vice versa, using pycogent. my reading of the docs suggests that i can just find the syntenic region for each exon in the alignment of human and mouse and that this should yield the orthologous exon coordina ...
python ensembl comparative written 8.1 years ago by User 933460 • updated 8.1 years ago by Biojl1.7k
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Comment: C: Haldane Map Function And Genetic Linkage
... This makes no sense, since if you have something that's roughly 100 Mb away, it can't be that the recombination frequency is around 40%. It should be far less. if snp A is 100 Mb away from snp B, what is their predicted recombination frequency? ...
written 8.1 years ago by User 933460
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Comment: C: Haldane Map Function And Genetic Linkage
... if I plug in 100 cM into the equation for r from http://statgen.ncsu.edu/qtlcart/manual/node46.html i still get that r = 0.5, which cannot be right. if snp A and snp B are 100 Mb apart on the same chromosome, they will not segregate independently ...
written 8.1 years ago by User 933460
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Comment: C: Haldane Map Function And Genetic Linkage
... so what would it be in this case? i am not sure i see the answer ...
written 8.1 years ago by User 933460
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Haldane Map Function And Genetic Linkage
... if i have two markers that are 100 Mb apart on the same chromosome, and i know that for my chromosome, centiMorgan to megaBase ratio is .9, then how many offspring in a generation can i expect to recombine between A and B? since 1 centiMorgan is roughly 1 megaBase in this case, and 1 centiMorgan is ...
linkage genetics snp written 8.1 years ago by User 933460 • updated 8.1 years ago by Haibao Tang3.0k

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